9CKV: Alpha5beta1 integrin

Cryo-EM structure of alpha5beta1 integrin in complex with NeoNectin. Determined by electron microscopy at 3.19 Å resolution. Released 17 Jul 2024.

Method: Electron microscopy
Resolution: 3.19 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 6,893
Mol. weight: 206.84 kDa
Ligands: MN, NAG, CA
Released: 17 Jul 2024

Explore 9CKV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CKV contains 26 α-helices and 69 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	1
β-strand	23-26	4	2
β-strand	34-39	6	2
β-strand	54-59	6	2
β-strand	68-69	2	2
β-strand	94-95	2	3
β-strand	104-108	5	4
β-strand	111-116	6	4
β-strand	120-122	3	3
β-strand	129-130	2	3
β-strand	134-139	6	4
β-strand	144-148	5	4
β-strand	169-172	4	5
β-strand	178-182	5	5
α-helix	185-188	4
β-strand	190	1	6
β-strand	191-195	5	5
α-helix	197-203	7
β-strand	217-218	2	5
α-helix	219-221	3
α-helix	224-226	3
β-strand	231	1	6
β-strand	235-238	4	7
β-strand	247-252	6	7
β-strand	261-265	5	7
β-strand	272-277	6	7
β-strand	289-292	4	8
β-strand	301-306	6	8
β-strand	310-312	3	9
β-strand	318-320	3	9
β-strand	323-327	5	8
β-strand	329	1	10
β-strand	334	1	10
β-strand	340-343	4	8
β-strand	355-359	5	11
β-strand	368-373	6	11
β-strand	382	1	12
β-strand	383-387	5	11
β-strand	400-402	3	11
α-helix	407-408	2
β-strand	415	1	12
β-strand	418-423	6	1
β-strand	432-437	6	1
β-strand	442-446	5	1

Chain B: 19 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	66-72	7	13
β-strand	96-103	8	13
β-strand	104	1	14
β-strand	105	1	15
β-strand	107	1	14
β-strand	109-116	8	15
α-helix	120-122	3
β-strand	123-130	8	16
α-helix	133-135	3
α-helix	139-156	18
β-strand	160-167	8	16
α-helix	173-175	3
α-helix	180-184	5
β-strand	194	1	17
α-helix	195-196	2
β-strand	200-206	7	16
α-helix	209-216	8
β-strand	222	1	17
β-strand	229	1	18
α-helix	231-240	10
α-helix	242-245	4
β-strand	251-258	8	16
β-strand	262	1	18
α-helix	267-271	5
α-helix	276-277	2
β-strand	283	1	19
β-strand	288	1	19
α-helix	290-292	3
α-helix	295-298	4
α-helix	299-309	11
β-strand	311-318	8	16
α-helix	322-331	10
β-strand	335-340	6	16
α-helix	345-356	12
β-strand	360-363	4	20
β-strand	364-366	3	13
α-helix	368-370	3
β-strand	373-380	8	15
α-helix	382-384	3
β-strand	386-388	3	15
α-helix	389-393	5
β-strand	394-398	5	20
β-strand	403-412	10	15
β-strand	421-427	7	13
β-strand	434-440	7	13

Chain C: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	21
α-helix	13-25	13
β-strand	30-32	3	21
β-strand	36-39	4	21
α-helix	44-57	14
β-strand	61-64	4	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin alpha-5	A	protein	1005	Homo sapiens	P08648 (AlphaFold model)
Integrin beta-1	B	protein	738	Homo sapiens	P05556 (AlphaFold model)
NeoNectin	C	protein	97	synthetic construct

Sequence of entity 1 (A), FASTA

>9CKV_1 Integrin alpha-5 (chains A)
MGSRTPESPLHAVQLRWGPRRRPPLLPLLLLLLPPPPRVGGFNLDAEAPAVLSGPPGSFF
GFSVEFYRPGTDGVSVLVGAPKANTSQPGVLQGGAVYLCPWGASPTQCTPIEFDSKGSRL
LESSLSSSEGEEPVEYKSLQWFGATVRAHGSSILACAPLYSWRTEKEPLSDPVGTCYLST
DNFTRILEYAPCRSDFSWAAGQGYCQGGFSAEFTKTGRVVLGGPGSYFWQGQILSATQEQ
IAESYYPEYLINLVQGQLQTRQASSIYDDSYLGYSVAVGEFSGDDTEDFVAGVPKGNLTY
GYVTILNGSDIRSLYNFSGEQMASYFGYAVAATDVNGDGLDDLLVGAPLLMDRTPDGRPQ
EVGRVYVYLQHPAGIEPTPTLTLTGHDEFGRFGSSLTPLGDLDQDGYNDVAIGAPFGGET
QQGVVFVFPGGPGGLGSKPSQVLQPLWAASHTPDFFGSALRGGRDLDGNGYPDLIVGSFG
VDKAVVYRGRPIVSASASLTIFPAMFNPEERSCSLEGNPVACINLSFCLNASGKHVADSI
GFTVELQLDWQKQKGGVRRALFLASRQATLTQTLLIQNGAREDCREMKIYLRNESEFRDK
LSPIHIALNFSLDPQAPVDSHGLRPALHYQSKSRIEDKAQILLDCGEDNICVPDLQLEVF
GEQNHVYLGDKNALNLTFHAQNVGEGGAYEAELRVTAPPEAEYSGLVRHPGNFSSLSCDY
FAVNQSRLLVCDLGNPMKAGASLWGGLRFTVPHLRDTKKTIQFDFQILSKNLNNSQSDVV
SFRLSVEAQAQVTLNGVSKPEAVLFPVSDWHPRDQPQKEEDLGPAVHHVYELINQGPSSI
SQGVLELSCPQALEGQQLLYVTRVTGLNCTTNHPINPKGLELDPEGSLHHQQKREAPSRS
SASSGPQILKCPEAECFRLRCELGPLHQQESQSLQLHFRVWAKTFLQREHQPFSLQCEAV
YKALKMPYRILPRQLPQKERQVATAVQWTKAEGSYGTGGLEVLFQ

Sequence of entity 2 (B), FASTA

>9CKV_2 Integrin beta-1 (chains B)
MNLQPIFWIGLISSVCCVFAQTDENRCLKANAKSCGECIQAGPNCGWCTNSTFLQEGMPT
SARCDDLEALKKKGCPPDDIENPRGSKDIKKNKNVTNRSKGTAEKLKPEDITQIQPQQLV
LRLRSGEPQTFTLKFKRAEDYPIDLYYLMDLSYSMKDDLENVKSLGTDLMNEMRRITSDF
RIGFGSFVEKTVMPYISTTPAKLRNPCTSEQNCTSPFSYKNVLSLTNKGEVFNELVGKQR
ISGNLDSPEGGFDAIMQVAVCGSLIGWRNVTRLLVFSTDAGFHFAGDGKLGGIVLPNDGQ
CHLENNMYTMSHYYDYPSIAHLVQKLSENNIQTIFAVTEEFQPVYKELKNLIPKSAVGTL
SANSSNVIQLIIDAYNSLSSEVILENGKLSEGVTISYKSYCKNGVNGTGENGRKCSNISI
GDEVQFEISITSNKCPKKDSDSFKIRPLGFTEEVEVILQYICECECQSEGIPESPKCHEG
NGTFECGACRCNEGRVGRHCECSTDEVNSEDMDAYCRKENSSEICSNNGECVCGQCVCRK
RDNTNEIYSGKFCECDNFNCDRSNGLICGGNGVCKCRVCECNPNYTGSACDCSLDTSTCE
ASNGQICNGRGICECGVCKCTDPKFQGQTCEMCQTCLGVCAEHKECVQCRAFNKGEKKDT
CTQECSYFNITKVESRDKLPQPVQPDPVSHCKEKDVDDCWFYFTYSVNGNNEVMVHVVEN
PECPTGPDDTSGLEVLFQ

Sequence of entity 3 (C), FASTA

>9CKV_3 NeoNectin (chains C)
MGLNDIFEAQKIEWHEGGSGGSELIIHGRGDFPSSELERLRERFERLGIKVRVDHKVLTL
IGISEEEAERLARELRKRGIWVEIRKGGSLEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	3
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
CA	Calcium ion	Ca	4

Primary citation

De Novo Design of Integrin alpha 5 beta 1 Modulating Proteins to Enhance Biomaterial Properties. Wang, X., Guillem-Marti, J., Kumar, S. et al. Adv Mater (2025) 37:e2500872-e2500872. DOI 10.1002/adma.202500872 · PubMed

Other PDB entries of the same protein (UniProt P08648 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4WK0 1.78 Å, Metal Ion and Ligand Binding of Integrin
4WJK 1.85 Å, Metal Ion and Ligand Binding of Integrin
9HMH 1.92 Å, Crystal structure of the Calf domains of Integrin Alpha5
4WK2 2.5 Å, Metal Ion and Ligand Binding of Integrin
4WK4 2.5 Å, Metal Ion and Ligand Binding of Integrin
9B9J 2.6 Å, Integrin alpha-5 beta-1 in complex with BIIG2 Fab
9P6S 2.61 Å, Cryo-EM structure of human integrin alpha5beta1 in complex with fibronectin (FN 7-10)
9B9K 2.7 Å, Integrin alpha-5 beta-1 in complex with MINT1526A Fab
9HMI 2.87 Å, Crystal structure of the Calf domains of Integrin Alpha5 in complex with angiopoietin2…
3VI3 2.9 Å, Crystal structure of alpha5beta1 integrin headpiece (ligand-free form)
3VI4 2.9 Å, Crystal structure of alpha5beta1 integrin headpiece in complex with RGD peptide
9DIA 2.97 Å, Cryo-EM structure of alpha5beta1 integrin in complex with NeoNectin candidate 2

Browse structure collections

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